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Biswas S, Kumar Bhagat G, Guha D, Bagchi A. Molecular characterization of the unusual peptide CORO1C-47aa encoded by the circular RNA and docking simulations with its binding partner. Gene 2023:147546. [PMID: 37286017 DOI: 10.1016/j.gene.2023.147546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/26/2023] [Accepted: 06/02/2023] [Indexed: 06/09/2023]
Abstract
Circular RNAs, which have covalently closed ends, are in the class of non-coding RNAs. Recent studies reveal that they are associated with various biochemical pathways. One such involvement of circular RNAs is in the onset of different types of cancers. Though the circular RNAs are known as non-coding RNAs, some of them are found to possess the capacities to code for proteins. One such circular RNA is hsa-circ-0000437 which is known to code for a short peptide referred to as CORO1C-47aa. The peptide has anti-angiogenic activity and is associated with the prevention of endometrial cancer. The peptide binds to the PAS-B domain of the Aryl hydrocarbon Receptor Nuclear Translocator (ARNT). However, till date only the amino acid sequence of the peptide is known and no structural details of the peptide are available. Therefore, in this work, our aim was to predict how the peptide would fold and what could be its possible ligand binding sites. We used computational tools to determine the structure of the peptide refined further by molecular dynamics simulations. We then performed molecular docking simulations of the peptide with its known binding partner ARNT to gain an insight into the modes of binding as the process is associated with endometrial cancer. The possible ligand binding sites along-with the natures of the possible other different ligands of the peptide were analyzed further. From this structure function analysis study, we tried to elucidate the plausible mechanism of the involvements of the peptide in the onset of endometrial cancer. This is the first report on the structural characterization of the peptide and its modes of interactions with the partner protein ARNT. This study may therefore be useful in determining the structures of new drug candidates for the treatment of endometrial cancer.
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Affiliation(s)
- Sima Biswas
- Department of Biochemistry & Biophysics, University of Kalyani, Kalyani-741235, Nadia, West Bengal, India
| | - Gaurav Kumar Bhagat
- Department of Biochemistry & Biophysics, University of Kalyani, Kalyani-741235, Nadia, West Bengal, India
| | - Dipanjan Guha
- Department of Biochemistry & Biophysics, University of Kalyani, Kalyani-741235, Nadia, West Bengal, India
| | - Angshuman Bagchi
- Department of Biochemistry & Biophysics, University of Kalyani, Kalyani-741235, Nadia, West Bengal, India.
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Sharko F, Rbbani G, Siriyappagouder P, Raeymaekers JAM, Galindo-Villegas J, Nedoluzhko A, Fernandes JMO. CircPrime: a web-based platform for design of specific circular RNA primers. BMC Bioinformatics 2023; 24:205. [PMID: 37208611 DOI: 10.1186/s12859-023-05331-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 05/11/2023] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND Circular RNAs (circRNAs) are covalently closed-loop RNAs with critical regulatory roles in cells. Tens of thousands of circRNAs have been unveiled due to the recent advances in high throughput RNA sequencing technologies and bioinformatic tools development. At the same time, polymerase chain reaction (PCR) cross-validation for circRNAs predicted by bioinformatic tools remains an essential part of any circRNA study before publication. RESULTS Here, we present the CircPrime web-based platform, providing a user-friendly solution for DNA primer design and thermocycling conditions for circRNA identification with routine PCR methods. CONCLUSIONS User-friendly CircPrime web platform ( http://circprime.elgene.net/ ) works with outputs of the most popular bioinformatic predictors of circRNAs to design specific circular RNA primers. CircPrime works with circRNA coordinates and any reference genome from the National Center for Biotechnology Information database).
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Affiliation(s)
- Fedor Sharko
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33/2, 119071, Moscow, Russia
- Limited Liability Company ELGENE, Malaya Kalitnikovskaya 16, 109029, Moscow, Russia
- National Research Center "Kurchatov Institute", 1st Akademika Kurchatova Square, 123182, Moscow, Russia
| | - Golam Rbbani
- Faculty of Biosciences and Aquaculture, Nord University, Universitetsalléen 11, PB 1490, 8049, Bodø, Norway
| | | | - Joost A M Raeymaekers
- Faculty of Biosciences and Aquaculture, Nord University, Universitetsalléen 11, PB 1490, 8049, Bodø, Norway
| | - Jorge Galindo-Villegas
- Faculty of Biosciences and Aquaculture, Nord University, Universitetsalléen 11, PB 1490, 8049, Bodø, Norway
| | - Artem Nedoluzhko
- Faculty of Biosciences and Aquaculture, Nord University, Universitetsalléen 11, PB 1490, 8049, Bodø, Norway.
- Paleogenomics Laboratory, European University at Saint Petersburg, 6/1A Gagarinskaya st., 191187, Saint Petersburg, Russia.
| | - Jorge M O Fernandes
- Faculty of Biosciences and Aquaculture, Nord University, Universitetsalléen 11, PB 1490, 8049, Bodø, Norway.
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Mookherjee T, Bagchi A, Ghosh R. In-silico studies to analyse the possible interactions of CircPPP1R12A translated peptide with Mst proteins. Biochem Biophys Res Commun 2022; 635:108-113. [DOI: 10.1016/j.bbrc.2022.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/01/2022] [Indexed: 11/29/2022]
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